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22  structures 164  species 3  interactions 1357  sequences 9  architectures

Family: Pou (PF00157)

Summary: Pou domain - N-terminal to homeobox domain

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POU domain Edit Wikipedia article

Pou domain - N-terminal to homeobox domain
Identifiers
Symbol Pou
Pfam PF00157
InterPro IPR000327
PROSITE PDOC00035
SCOP 1oct
SUPERFAMILY 1oct

POU (pronounced 'pow') is a family of proteins that have well-conserved homeodomains.[1]

Etymology[edit]

The acronym POU is derived from the names of three transcription factors:

Diversity[edit]

POU domain genes have been described in organisms as divergent as Caenorhabditis elegans, Drosophila, Xenopus, zebrafish and human but have not been yet identified in plants and fungi.

There is a surprisingly high degree of amino acid sequence conservation (37%-42%) of POU homeodomains to the transcriptional regulator comS, the competence protein from the gram positive prokaryote Bacillus subtilis.[2] Interestingly, akin to the way that POU homeodomain regulators lead to tissue differentiation in metazoans, this transcription factor is critical for differentiation of a subpopulation of B. subtilis into a state of genetic competence.

Function[edit]

POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is derived from the names of three transcription factors, the pituitary-specific [[Pituitary-specific positive transcription factor 1|Pit-1]], the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been described in organisms as divergent as Caenorhabditis elegans, Drosophila, Xenopus, zebrafish and human but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system[3] and the development of an organism.[4] Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2),[5][6] and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1).

Structure[edit]

The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327), while the C-terminal subunit is a homeobox domain (IPR007103). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions.[7] The subdomains are connected by a flexible linker.[8][9][10] In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family.[8][9]

Examples[edit]

Human genes encoding proteins containing the POU domain include:

References[edit]

  1. ^ {{cite journal | author = Phillips K, Luisi B | title = The virtuoso of versatility: POU proteins that flex to fit | journal = J. Mol. Biol. | volume = 302 | issue = 5 | pages = 1023–39 | year = 2000 | pmid = 11183772 | doi = 10.1006/jmbi.2000.4107 }}
  2. ^ D'Souza C, Nakano MM, Zuber P (September 1994). "Identification of comS, a gene of the srfA operon that regulates the establishment of genetic competence in Bacillus subtilis". Proc. Natl. Acad. Sci. U.S.A. 91 (20): 9397–401. doi:10.1073/pnas.91.20.9397. PMC 44819. PMID 7937777. 
  3. ^ Assa-Munt N, Mortishire-Smith RJ, Aurora R, Herr W, Wright PE (1993). "The solution structure of the Oct-1 POU-specific domain reveals a striking similarity to the bacteriophage lambda repressor DNA-binding domain". Cell 73 (1): 193–205. doi:10.1016/0092-8674(93)90171-L. PMID 8462099. 
  4. ^ Rosenfeld MG, Andersen B (2001). "POU domain factors in the neuroendocrine system: lessons from developmental biology provide insights into human disease". Endocr. Rev. 22 (1): 2–35. doi:10.1210/er.22.1.2. PMID 11159814. 
  5. ^ Petryniak B, Thompson CB, Staudt LM, Postema CE, McCormack WT (1990). "Characterization of chicken octamer-binding proteins demonstrates that POU domain-containing homeobox transcription factors have been highly conserved during vertebrate evolution". Proc. Natl. Acad. Sci. U.S.A. 87 (3): 1099–1103. doi:10.1073/pnas.87.3.1099. PMC 53418. PMID 1967834. 
  6. ^ Hirsh J, Johnson WA (1990). "Binding of a Drosophila POU-domain protein to a sequence element regulating gene expression in specific dopaminergic neurons". Nature 343 (6257): 467–470. doi:10.1038/343467a0. PMID 1967821. 
  7. ^ {{cite journal |author=Mathis JM, Simmons DM, He X, Swanson LW, Rosenfeld MG |title=Brain 4: a novel mammalian POU domain transcription factor exhibiting restricted brain-specific expression |journal=EMBO J. |volume=11 |issue=7 |pages=2551–2561 |year=1992 |pmid=1628619 |pmc=556730}}
  8. ^ a b Phillips K, Luisi B (2000). "The virtuoso of versatility: POU proteins that flex to fit". J. Mol. Biol. 302 (5): 1023–1039. doi:10.1006/jmbi.2000.4107. PMID 11183772. 
  9. ^ a b Pabo CO, Aurora R, Herr W, Klemm JD, Rould MA (1994). "Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules". Cell 77 (1): 21–32. doi:10.1016/0092-8674(94)90231-3. PMID 8156594. 
  10. ^ Rosenfeld MG, Aggarwal AK, Li P, Jacobson EM, Leon-del-Rio A (1997). "Structure of Pit-1 POU domain bound to DNA as a dimer: unexpected arrangement and flexibility". Genes Dev. 11 (2): 198–212. doi:10.1101/gad.11.2.198. PMID 9009203. 

This article incorporates text from the public domain Pfam and InterPro IPR000327

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External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000327

POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [PUBMED:8462099] and the development of an organism [PUBMED:11159814]. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [PUBMED:1967834, PUBMED:1967821], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1).

The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (INTERPRO), while the C-terminal subunit is a homeobox domain (INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions [PUBMED:1628619]. The subdomains are connected by a flexible linker [PUBMED:11183772, PUBMED:8156594, PUBMED:9009203]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [PUBMED:11183772, PUBMED:8156594].

This entry represents the POU-specific subunit of the POU domain.

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan HTH (CL0123), which has the following description:

This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif.

The clan contains the following 202 members:

AphA_like Arg_repressor B-block_TFIIIC Bac_DnaA_C BetR Bot1p BrkDBD CENP-B_N Cro Crp DDRGK Dimerisation DUF1133 DUF1153 DUF1323 DUF134 DUF1441 DUF1492 DUF1495 DUF1670 DUF1804 DUF1836 DUF1870 DUF2089 DUF2250 DUF2316 DUF3116 DUF3853 DUF387 DUF3908 DUF4095 DUF4364 DUF739 DUF742 DUF977 E2F_TDP ELK Ets Exc F-112 FaeA Fe_dep_repr_C Fe_dep_repress FeoC Ftsk_gamma FUR GcrA GerE GntR HARE-HTH HemN_C Homeobox Homeobox_KN Homez HrcA_DNA-bdg HSF_DNA-bind HTH_1 HTH_10 HTH_11 HTH_12 HTH_13 HTH_15 HTH_16 HTH_17 HTH_18 HTH_19 HTH_20 HTH_21 HTH_22 HTH_23 HTH_24 HTH_25 HTH_26 HTH_27 HTH_28 HTH_29 HTH_3 HTH_30 HTH_31 HTH_32 HTH_33 HTH_34 HTH_35 HTH_36 HTH_37 HTH_38 HTH_39 HTH_40 HTH_41 HTH_42 HTH_43 HTH_45 HTH_5 HTH_6 HTH_7 HTH_8 HTH_9 HTH_AraC HTH_AsnC-type HTH_CodY HTH_Crp_2 HTH_DeoR HTH_IclR HTH_Mga HTH_OrfB_IS605 HTH_psq HTH_Tnp_1 HTH_Tnp_1_2 HTH_Tnp_4 HTH_Tnp_IS1 HTH_Tnp_IS630 HTH_Tnp_ISL3 HTH_Tnp_Mu_1 HTH_Tnp_Mu_2 HTH_Tnp_Tc3_1 HTH_Tnp_Tc3_2 HTH_Tnp_Tc5 HTH_WhiA HxlR IF2_N KorB LacI LexA_DNA_bind LZ_Tnp_IS481 MADF_DNA_bdg MarR MarR_2 Med9 MerR MerR-DNA-bind MerR_1 MerR_2 Mga Mnd1 Mor MotA_activ MRP-L20 Myb_DNA-bind_2 Myb_DNA-bind_3 Myb_DNA-bind_4 Myb_DNA-bind_5 Myb_DNA-bind_6 Myb_DNA-binding Neugrin NUMOD1 OST-HTH P22_Cro PaaX PadR PAX PCI PCI_Csn8 Penicillinase_R Phage_AlpA Phage_antitermQ Phage_CI_repr Phage_CII Phage_rep_org_N Phage_terminase Pou Pox_D5 PuR_N Put_DNA-bind_N Rap1-DNA-bind Rep_3 RepA_C RepA_N RepC RepL Replic_Relax RFX_DNA_binding Ribosomal_S25 Rio2_N RNA_pol_Rpc34 RP-C RPA RPA_C RQC Rrf2 RTP SAC3_GANP SgrR_N Sigma54_CBD Sigma54_DBD Sigma70_ECF Sigma70_r2 Sigma70_r3 Sigma70_r4 Sigma70_r4_2 SpoIIID Sulfolobus_pRN TBPIP Terminase_5 TetR_N TFIIE_alpha Tn916-Xis Trans_reg_C TrfA TrmB Trp_repressor UPF0122 z-alpha

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(20)
Full
(1357)
Representative proteomes NCBI
(1331)
Meta
(1)
RP15
(111)
RP35
(158)
RP55
(327)
RP75
(578)
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Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(20)
Full
(1357)
Representative proteomes NCBI
(1331)
Meta
(1)
RP15
(111)
RP35
(158)
RP55
(327)
RP75
(578)
Alignment:
Format:
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Sequence:
Gaps:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(20)
Full
(1357)
Representative proteomes NCBI
(1331)
Meta
(1)
RP15
(111)
RP35
(158)
RP55
(327)
RP75
(578)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite
Previous IDs: pou;
Type: Domain
Author: Sonnhammer ELL
Number in seed: 20
Number in full: 1357
Average length of the domain: 69.20 aa
Average identity of full alignment: 59 %
Average coverage of the sequence by the domain: 18.40 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.0 21.5
Noise cut-off 20.9 20.9
Model length: 75
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

HMG_box Pou Homeobox

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Pou domain has been found. There are 22 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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